Locus 4168

Sequence ID	2L_DroMel_CAF1
Location	11,965,904 – 11,966,049
Length	145
Max. P	0.977340

overview

Window 4

Location	11,965,904 – 11,966,009
Length	105
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	90.73
Mean single sequence MFE	-45.54
Consensus MFE	-34.68
Energy contribution	-34.92
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.82
Structure conservation index	0.76
SVM decision value	1.79
SVM RNA-class probability	0.977340
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11965904 105 + 22407834
UCUUUUGCGGUUGCGCUGCA-----UCGCUCGAUUCGAAUGGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGGGAUAUUGGCCGAAAGGCACAGCAGCUUAGCCCAGG
....(((.(((((.((((((-----((.((....(((.(((((((((((......))).)))))))).))).)).)))..(((((....))).))))))).)))))))). ( -45.10)
>DroSec_CAF1 185292 109 + 1
UCUUCUGCGGUUGCGCUGCAUCGCAUCGCUCGAUUCGAAUGGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGGGAUGUUGGCCCAAAGGCACAGCAGCUUAGC-CAGG
.....(((((.....)))))(((.(((....))).)))(((((((((((......))).))))))))(((((..((.((((((((....))).))))).))..))-))). ( -47.00)
>DroSim_CAF1 151644 109 + 1
UCUUCUGCGGUUGCGCUGCAUCGCAUCGCUCGUUUCGAAUGGGCAGCCAGAAAACUGGUUUGCCCAUCUGGCAGGGAUGUUGGCCCAAAGGCACAGCAGCUUAGC-CAGG
......(((((.(((......)))))))).........((((((((((((....)))).))))))))(((((..((.((((((((....))).))))).))..))-))). ( -48.60)
>DroEre_CAF1 160036 104 + 1
UCGGCUGUGGUUGCGCCGCA-----UCGCUCGAUUCGAAUGGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGGGAAGUUGGCCCAAAGGCAGAGCAGCUUGGC-CAGG
((((((((((.....)))))-----..)).))).....(((((((((((......))).))))))))(((((..((..(((.(((....)))..)))..))..))-))). ( -43.00)
>DroYak_CAF1 156424 104 + 1
ACGGCUGUGGUUGCGCUGCA-----UCGCUCGAUUCGAAUGGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGUGAAGUUGGCCCAAAGGCAGAGCAGCUUAGC-CAGG
..(((((.((((((((((((-----((....))).((.(((((((((((......))).)))))))).))))))).......(((....)))...))))))))))-)... ( -44.00)
>consensus
UCUUCUGCGGUUGCGCUGCA_____UCGCUCGAUUCGAAUGGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGGGAUGUUGGCCCAAAGGCACAGCAGCUUAGC_CAGG
........(((((.(((((.........(((...(((.(((((((((((......))).)))))))).)))..)))......(((....)))...))))).)))).)... (-34.68 = -34.92 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	11,965,939 – 11,966,049
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	91.77
Mean single sequence MFE	-43.56
Consensus MFE	-31.58
Energy contribution	-33.02
Covariance contribution	1.44
Combinations/Pair	1.03
Mean z-score	-3.61
Structure conservation index	0.72
SVM decision value	1.52
SVM RNA-class probability	0.960726
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11965939 110 + 22407834
GGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGGGAUAUUGGCCGAAAGGCACAGCAGCUUAGCCCAGGAACAGUGUCCCGGGGUAACGAAGCUAUAAAAUCACUGCAG
(((((((((......))).)))))).....((((.(((.((((((....))).))).(((((.((((.(((......)))..))))....))))).....))).)))).. ( -44.20)
>DroSec_CAF1 185332 109 + 1
GGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGGGAUGUUGGCCCAAAGGCACAGCAGCUUAGC-CAGGAACAGUGUCCCGUGGUAACGAAGCUAUAAAAUCACUGCAG
(((((((((......))).)))))).((((((..((.((((((((....))).))))).))..))-))))..(((((....(((((......))))).....)))))... ( -44.90)
>DroSim_CAF1 151684 109 + 1
GGGCAGCCAGAAAACUGGUUUGCCCAUCUGGCAGGGAUGUUGGCCCAAAGGCACAGCAGCUUAGC-CAGGAACAGUGUCCCGUGGUAACGAAGCUAUAAAAUAACUGCAG
((((((((((....)))).)))))).((((((..((.((((((((....))).))))).))..))-))))..((((.....(((((......)))))......))))... ( -44.80)
>DroEre_CAF1 160071 109 + 1
GGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGGGAAGUUGGCCCAAAGGCAGAGCAGCUUGGC-CAGGAACAGUGUCCUGGGGAAACGAAGCUAUAAAAUCACUGGAC
(((((((((......))).))))))......(((.((.(((.(((....)))..)))(((((..(-(((((......))))))(....).)))))......)).)))... ( -38.90)
>DroYak_CAF1 156459 109 + 1
GGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGUGAAGUUGGCCCAAAGGCAGAGCAGCUUAGC-CAGGAACAGUGUCCUGGGGAAACGGGGCCAUAAAAUCACUCGGC
(((((((((......))).))))))..(((..(((((...((((((..((((......))))..(-(((((......))))))(....).)))))).....)))))))). ( -45.00)
>consensus
GGGCAGCCAAAAAACUGGUUUGCCCAUCUGGCAGGGAUGUUGGCCCAAAGGCACAGCAGCUUAGC_CAGGAACAGUGUCCCGGGGUAACGAAGCUAUAAAAUCACUGCAG
(((((((((......))).)))))).((((((.(((.((((((((....))).))))).))).)).))))..(((((......((........)).......)))))... (-31.58 = -33.02 +   1.44)

alignment

secondary structure

dotplot

Window 6

Location	11,965,939 – 11,966,049
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	91.77
Mean single sequence MFE	-35.42
Consensus MFE	-27.52
Energy contribution	-28.16
Covariance contribution	0.64
Combinations/Pair	1.10
Mean z-score	-1.60
Structure conservation index	0.78
SVM decision value	0.23
SVM RNA-class probability	0.645703
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11965939 110 - 22407834
CUGCAGUGAUUUUAUAGCUUCGUUACCCCGGGACACUGUUCCUGGGCUAAGCUGCUGUGCCUUUCGGCCAAUAUCCCUGCCAGAUGGGCAAACCAGUUUUUUGGCUGCCC
((((((.(((.(((((((..(.(((.(((((((......))))))).))))..)))))(((....))).)).))).))).)))..(((((..((((....)))).))))) ( -39.20)
>DroSec_CAF1 185332 109 - 1
CUGCAGUGAUUUUAUAGCUUCGUUACCACGGGACACUGUUCCUG-GCUAAGCUGCUGUGCCUUUGGGCCAACAUCCCUGCCAGAUGGGCAAACCAGUUUUUUGGCUGCCC
((((((.(((...(((((..(.((((((.(((((...)))))))-).))))..)))))(((....)))....))).))).)))..(((((..((((....)))).))))) ( -34.80)
>DroSim_CAF1 151684 109 - 1
CUGCAGUUAUUUUAUAGCUUCGUUACCACGGGACACUGUUCCUG-GCUAAGCUGCUGUGCCUUUGGGCCAACAUCCCUGCCAGAUGGGCAAACCAGUUUUCUGGCUGCCC
((((((.......(((((..(.((((((.(((((...)))))))-).))))..)))))(((....)))........))).)))..(((((..((((....)))).))))) ( -34.70)
>DroEre_CAF1 160071 109 - 1
GUCCAGUGAUUUUAUAGCUUCGUUUCCCCAGGACACUGUUCCUG-GCCAAGCUGCUCUGCCUUUGGGCCAACUUCCCUGCCAGAUGGGCAAACCAGUUUUUUGGCUGCCC
((((((.((......(((...((((..((((((......)))))-)..)))).)))..(((....))).....)).)))...)))(((((..((((....)))).))))) ( -30.20)
>DroYak_CAF1 156459 109 - 1
GCCGAGUGAUUUUAUGGCCCCGUUUCCCCAGGACACUGUUCCUG-GCUAAGCUGCUCUGCCUUUGGGCCAACUUCACUGCCAGAUGGGCAAACCAGUUUUUUGGCUGCCC
((..(((((.....((((((.((((..((((((......)))))-)..)))).((...))....))))))...))))))).....(((((..((((....)))).))))) ( -38.20)
>consensus
CUGCAGUGAUUUUAUAGCUUCGUUACCCCGGGACACUGUUCCUG_GCUAAGCUGCUGUGCCUUUGGGCCAACAUCCCUGCCAGAUGGGCAAACCAGUUUUUUGGCUGCCC
..((((.((.....((((((.((.....(((((......))))).)).))))))....(((....))).....)).)))).....(((((..((((....)))).))))) (-27.52 = -28.16 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:25 2006